The BioBricks Foundation:Workshop2/Live Notes

Drew's introduction (1:20 PST)

Roll Call:

• Igor Samulseon: Will graduate soon=
• Hillary Creely: Three Words
• Peter Mooney: Open Source Entrepreneurship
• Nick Earnt: Synthesize life effectively
• Tanny Cooks: where biobricks stand
• Chris Voigt: Genetic Engineering Bacteria
• Chris Anderson: Foundational Technologies Application
• Chris MASON: New Organisms, Yay
• Scott Mohr: Science is Fun
• Randy Rettberg: Used to be a computer guy
• Leanord Catz: Research Director of SynBERC
• Carline Ajo-Franklin: Synthetic Biology for nanotechnology
• ???
• Frasier Cunninghanm: Science Political policy
• Mac Cowell: open source biology
• Jason Morrison: computer science convert
• Rachel Wellhousen: Human Practices THURST
• Literature Based Research
• ?
• tom Knight: Engineering Simple Life
• Goatham Mukunda: Secuyrity Strategy & Politics
• Austin Che: Crazy DNA hacker
• Marrian McCormic: ?
• Carl: Venture Capital, go biobricks
• ?
• Ken Oye: Anti-commons kills synergism and investment
• Herbert Sauro: science *& sbml
• sean slate: SB & Evoltuion

Computational systems bio

• Tallis ?: Go Obama Go
• Ben ?: Anthropology SB
• ? : Black Swan Event
• Kevin Costa: Social Technocrat, HI
• ? : Grad Student Again
• John Dueber: Engineering Protein Devices
• Lucks: Still Learning Biology
• Barry Canton: Making bioengineering easier
• Reshma: Need A Job
• Christina: Molecular & systems engineering
• ? : Historian SB
• ? : Please Drive Me Crazy
• ?
• Julie Norville engineering protein crystals
• Ralph Santos: Long-winded email writer
• ?: Ethics by design
• Kate Spohr: education bottom up
• Dave Urdell: makes gmos safer

? Mony: wanderer, coder, immunologist (phone)

Drew's BG

• to ensure Biobricks exist as available components and can be shared and used
• if you don't like these rules, discuss and change them
• 300 members
• Technical group
• legal group
• even more volunteers
• educational / outreach group
• Volunteer board (tom, randy, pam, chris voigt)

• Existence reason: Free Biobrick Parts
  • (Move away from balkanized economy of genetic widgets to an open economy of freely available parts that work together)

• No obvious legal framework

• Not clear what a standard biological part is
  • beyond first draft (a la TK)

• Hence, these workshops - let's work on the legal framework and technical standards. That way, many more people than the BBF can choose to use and contribute to the collection of standard biological parts

Standards

• There's a mailing list

• At BBF workshop 1, the group produced a shopping list of Requested Technical standards: 21 items long. It included requests for standards for Assembling parts, for sharing parts on computer networks, for ordering DNA from synthesis companies, for searching parts, for characterizing them, safety standards, IP standards, for hiding & abstracting information, for identifying release level, etc.

There was an interesting "A Ha" moment for drew at the iGEM 2007 Jamboree. The Melbourne team presented a device that taught new biology, that worked, that met the BBa standard, and in principle could immediately be used with other BBa Standard parts. They built a buoyancy device. It was new, standardized, and could be used.

Also, the UCSF team, apprehending the competitive nature of the iGEM competition and the timeframe available, decided they would be better off developing and testing a whole series of parts that met a different standard that was ideal for the specifics of those to operations. They were successful, and unsuccessful - their parts and devices worked, for the most part, but they didn't meet the BBa standard. So, the BBa standard has limitations. That's ok - we should make an incrementally better version.

Ok, now let's watch Jason Kelly's video (he couldn't be here today). It expresses his position on standardized measurement methods and provides an overview of a promoter and rbs measurement kit he has devised. See it here: http://video.google.com/googleplayer.swf?docId=3783852973289336417&hl=en

See the BBF Technical Standards Setting Process.

So, Jason has demonstrated one working example of the promoter & rbs measurement standard. Caroline Ajo-Franklin mentioned that just yesterday she duplicated his example and the data agreed within 5%. The writeup is in the works.

Discussion

• Beads for Yeast? Chris Voigt
• Different standards for different dynamic ranges?
• Caroline: "on the basis of our calibration, I think that's a worthy concern, but on the basis of our calibration I think we have a good dynamic range."
• Randy: "In the early days of the internet, people would be making devices. Then the would have connect-a-thons, where they would try to connect their machine to one another's. Success would excite these engineers. We should try to have similar events. This would start to kill the presumption that in biology, every case is different. This development of consistency is a bedrock on which all these standards are based."
• Drew: The BBF provides a framework to support this.

So I don't have anything else to say, and we don't have any business to report (no tangible new standards to present), so let's spend the next 45 minutes in ad-hoc Birds of a Feather sessions. Consider the The_BioBricks_Foundation:Standards/Technical#Possible_New_Technical_Standards_Projects

Notes:

• Talk:The_BioBricks_Foundation:Workshop2/Functional_Measurement_Standards
• The_BioBricks_Foundation:Workshop2/New_Parts
• Talk:The_BioBricks_Foundation:Workshop2/Part_Data_Model